X-9891092-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBS2_Supporting
The NM_001649.4(SHROOM2):c.433G>A(p.Gly145Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000639 in 1,204,915 control chromosomes in the GnomAD database, including 1 homozygotes. There are 26 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001649.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000445 AC: 5AN: 112457Hom.: 0 Cov.: 25 AF XY: 0.0000289 AC XY: 1AN XY: 34603
GnomAD3 exomes AF: 0.000132 AC: 22AN: 166204Hom.: 0 AF XY: 0.000168 AC XY: 9AN XY: 53660
GnomAD4 exome AF: 0.0000659 AC: 72AN: 1092408Hom.: 1 Cov.: 35 AF XY: 0.0000697 AC XY: 25AN XY: 358490
GnomAD4 genome AF: 0.0000444 AC: 5AN: 112507Hom.: 0 Cov.: 25 AF XY: 0.0000288 AC XY: 1AN XY: 34663
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at